Preheat oven: 350°F (175°C). Line a muffin tin with 12 liners.
Make the cream cheese filling: Beat softened cream cheese, sugar, and vanilla until smooth and creamy. Set aside.
Mix dry ingredients: Whisk flour, pumpkin pie spice, cinnamon, baking powder, baking soda, and salt in a medium bowl.
Mix wet ingredients: In a large bowl, whisk pumpkin puree, eggs, sugars, oil, and vanilla until smooth. Stir in collagen if using.
Combine: Gently fold dry ingredients into wet until just combined. Do not overmix.
Assemble muffins: Fill each muffin liner ⅔ full with batter. Drop 1 tablespoon of cream cheese filling into the center, pressing lightly. Sprinkle pepitas on top.
Bake: 18–22 minutes, or until a toothpick inserted into the pumpkin muffin part comes out clean. Cool slightly before serving.